TPR packing analysis and 3D modeling for the HAT domain of human crooked neck protein

Human crooked neck protein (hcrn) containing 17 HAT or TPR repeats plays a role in pre-mRNA processing. Conserved residues in the TPR consensus sequence of 34 aa were found at helical packing interface and pro32 which breaks the second helix. The crn TPR helical hairpins were built on consensus TPR 3d template and packed side by side to form the overall superhelical structure. The models underwent a series of energy minimizing refinements and molecular dynamics simulations under constrains of holding each helical structure together but allow individual helix to spin around its own axis. The refined structures preserved the main characteristics of TPR superhelical fold with every 7 TPR units forming a complete repeat. The knob-hole rule was satisfied in majority of helix-helix packing. The models indicated that hcrn exerts its function in either mRNA processing or DNA duplication by mediating protein-protein interaction in a complex assembly.